Last modified by puchades on 2021/11/16 09:11
From version 5.1
edited by puchades
on 2020/03/25 17:04
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To version 2.3
edited by puchades
on 2020/03/25 15:16
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1 1  == Nutil Quantifier ==
2 2  
3 -A detailed Nutil user manual is included when downloading the software.
3 +A detailed Nutil user manual
4 4  
5 -[[image:Quantifier.PNG]]
5 +Lorem ipsum dolor sit amet, consectetur adipiscing elit, sed do eiusmod tempor incididunt ut labore et dolore magna aliqua. Ut enim ad minim veniam, quis nostrud exercitation ullamco laboris nisi ut aliquip ex ea commodo consequat. Duis aute irure dolor in reprehenderit in voluptate velit esse cillum dolore eu fugiat nulla pariatur. Excepteur sint occaecat cupidatat non proident, sunt in culpa qui officia deserunt mollit anim id est laborum.
6 6  
7 -**Basic steps:**
7 +>This is a quote. You can add a quote by selecting some text and clicking the quote button in the editor.
8 8  
9 -**//Quantifier//** locates and quantifies labelling identified by segmentation in rodent brain section images (mouse or rat). It requires the following input:
9 +Lorem ipsum dolor sit amet, consectetur adipiscing elit, sed do eiusmod tempor incididunt ut labore et dolore magna aliqua. Ut enim ad minim veniam, quis nostrud exercitation ullamco laboris nisi ut aliquip ex ea commodo consequat. Duis aute irure dolor in reprehenderit in voluptate velit esse cillum dolore eu fugiat nulla pariatur. Excepteur sint occaecat cupidatat non proident, sunt in culpa qui officia deserunt mollit anim id est laborum.
10 10  
11 -(% start="1" style="list-style-type:decimal" %)
12 -1. **Segmentations with the labeling displayed in one RGB colour**
11 +=== H3 Headings Will Appear In The Table of Content ===
13 13  
14 -**Requirement:**
13 +==== You can also add images ====
15 15  
16 -* must be 24-bit RGB images in PNG format
17 -* same proportions as the images used in QuickNII to generate the atlas maps (can be a different size)
18 -* **//Quantifier //**is only able to extract one RGB colour at a time. Apply one RBG colour to all of the objects of interest, and specify this colour code in the //Excel template//.
15 +[[image:Collaboratory.Apps.Article.Code.ArticleSheet@placeholder.jpg]]
19 19  
20 -To generate the segmentations we recommend the //Pixel and// //Object Classification workflows// in the //ilastik// software (//ilastik.org//). However, any image analysis software may be used.
17 +Photo by David Clode
21 21  
22 -(% start="2" %)
23 -1. **Customised anatomical atlas maps**
19 +==== Or code ====
24 24  
25 -Generate the atlas maps in FLAT format with the //QuickNII //software
21 +Code blocks can be added by using the code macro:
26 26  
27 -(% start="3" %)
28 -1. **Anchored XML** file generated with the //QuickNII// software.
29 -1. **Reference atlas label file** (in LABEL format) corresponding to the relevant atlas. The following reference atlases are included in the //Nutil// package (in the “Labels” folder). 
23 +{{code language="python"}}
24 +x = 1
25 +if x == 1:
26 + # indented four spaces
27 + print("x is 1.")
28 +{{/code}}
30 30  
31 -[[image:Illustration seg_flat_files.png||height="254" width="500"]]
32 -
33 -
34 -
30 +(% class="wikigeneratedid" id="HH4Won27tAppearinToC" %)
31 +
Illustration seg_flat_files.png
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